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Subcellular pharmacokinetic measurements have informed the study of central nervous system (CNS)–acting drug mechanisms. Recent investigations have been enhanced by the use of genetically encoded fluorescent biosensors for drugs of interest at the plasma membrane and in organelles. We describe screening and validation protocols for identifying hit pairs comprising a drug and biosensor, with each screen including 13–18 candidate biosensors and 44–84 candidate drugs. After a favorable hit pair is identified and validated via these protocols, the biosensor is then optimized, as described in other papers, for sensitivity and selectivity to the drug. We also show sample hit pair data that may lead to future intensity-based drug-sensing fluorescent reporters (iDrugSnFRs). These protocols will assist scientists to use fluorescence responses as criteria in identifying favorable fluorescent biosensor variants for CNS-acting drugs that presently have no corresponding biosensor partner. This protocol was validated in: eLife (2022), DOI: 10.7554/eLife.74648 Graphical abstract [Image: see text]

RF sheath heating as well as secondary electron acceleration play important role in the radio-frequency (RF) hollow cathode discharge (HCD). HCDs form in cylindrical cavities in the cathode, and one can use an array of such cavities to create large area HCDs. The plasma in the hollow cavities can become more intense due to the hollow cathode effect (HCE) under certain conditions. In this study, a single hollow cathode hole is modeled using Particle-in-Cell/Monte Carlo simulation. In this model, using charge density of particles, Poisson equation is solved for electric potential, which yields the electric field. Using this electric field, all charged particles’ velocities are updated and the particles are moved. This PIC code considers particle collisions with each other and with neutral fluid using a Monte Carlo model. Statistics of these collisions are used to determine how electron energy is dissipated in the plasma. RF hollow cathode behavior is characterized for different hole size, pressure and RF voltage. The plasma penetrates inside the hollow cathode hole with increase in pressure, leading to HCE enhancement. With increase in hole size, plasma penetrates further into the hole at a given pressure. At high RF voltage, plasma density enhancement is limited as plasma spreads over larger volume. To evaluate the effect of RF sheath heating, the hollow cathode discharge is modeled at different frequencies ranging from high to low frequency. To understand the importance of secondary electron acceleration on the discharge, we modeled the discharge for different secondary electron emission coefficients. In order to determine the collective behavior of an array of hollow cathode holes, a reduced order model based on a neural network is developed utilizing the detailed PIC modeling results. Preliminary results using the reduced order model are also presented.

Nicotine dependence is thought to arise in part because nicotine permeates into the endoplasmic reticulum (ER), where it binds to nicotinic receptors (nAChRs) and begins an “inside-out” pathway that leads to up-regulation of nAChRs on the plasma membrane. However, the dynamics of nicotine entry into the ER are unquantified. Here, we develop a family of genetically encoded fluorescent biosensors for nicotine, termed iNicSnFRs. The iNicSnFRs are fusions between two proteins: a circularly permutated GFP and a periplasmic choline-/betaine-binding protein engineered to bind nicotine. The biosensors iNicSnFR3a and iNicSnFR3b respond to nicotine by increasing fluorescence at [nicotine] 75%. Reducing nicotine intake by 10-fold decreases activation to ∼20%. iNicSnFR3a and iNicSnFR3b also sense the smoking cessation drug varenicline, revealing that varenicline also permeates into the ER within seconds. Our iNicSnFRs enable optical subcellular pharmacokinetics for nicotine and varenicline during an early event in the inside-out pathway.

Herein we report the one-pot synthesis of a fluorescent polymer-like material (pCD) by exploiting ruthenium-doped carbon dots (CDs) as building blocks. The unusual spectral profiles of pCDs with double-humped periodic excitation dependent photoluminescence (EDPL), and the regular changes in their corresponding average lifetime indicate the formation of high energy donor states and low energy aggregated states due to the overlap of molecular orbitals throughout the chemically switchable π-network of CDs on polymerization. To probe the electronic distribution of pCDs, we have investigated the occurrence of photoinduced electron transfer with a model electron acceptor, menadione using transient absorption technique, corroborated with low magnetic field, followed by identification of the transient radical ions generated through electron transfer. The experimentally obtained B1/2 value, a measure of the hyperfine interactions present in the system, indicates the presence of highly conjugated π-electron cloud i...

Herein we have engineered a smart nuclear targeting thiol-modified riboflavin-gold nano assembly, RfS@AuNPs, which accumulates selectively in the nucleus without any nuclear-targeting peptides (NLS/RGD) and shows photophysically in vitro DNA intercalation. A theoretical model using Molecular Dynamics has been developed to probe the mechanism of formation and stability as well as dynamics of the RfS@AuNPs in aqueous solution and within the DNA microenvironment. The RfS@AuNPs facilitate the binucleated cell formation that is reflected in the significant increase of DNA damage marker, γ-H2AX as well as the arrest of most of the HeLa cells at the pre-G1 phase indicating cell death. Moreover, a significant upregulation of apoptotic markers confirms that the cell death occurs through the apoptotic pathway. Analyses of the microarray gene expression of RfS@AuNPs treated HeLa cells show significant alterations in vital biological processes necessary for cell survival. Taken together, our study reports a unique nuclear targeting mechanism through targeting the riboflavin receptors, which are upregulated in cancer cells and induce apoptosis in the targeted cells.

Strategies for simultaneous detection and detoxification of Hg^(2+) using a single sensor from biological and environmental samples are limited and have not been realized in living organisms so far. We report a highly selective, small molecule “turn-on” fluorescent sensor, PYDMSA, based on the cationic dye Pyronin Y (PY) and chelating agent meso-2,3-dimercaptosuccinic acid (DMSA) for the simultaneous detection and detoxification of inorganic mercury (Hg^(2+)). After Hg^(2+) detection, concomitant detoxification was carried out with sufficient efficacy in living samples, which makes the sensor unique. PYDMSA exhibits high selectivity for Hg^(2+) over other competing metal ions with an experimental detection limit of ∼300 pM in aqueous buffer solution. When PYDMSA reacts with Hg2+, the CS–C^9 bond in the sensor gets cleaved. This results in the “turn-on” response of the fluorescence probe with a concomitant release of one equivalent of water-soluble Hg^(2+)–DMSA complex which leads to a synchronous detoxifying effect. The sensor by itself is nontoxic to cells in culture and has been used to monitor the real-time uptake of Hg^(2+) in live cells and zebrafish larvae. Thus, PYDMSA is a unique sensor which can be used to detect and detoxify mercury at the same time in living samples.

Self-organized structures that are spread perpendicular to the radio frequency (RF) current direction have been observed in low temperature RF capacitively coupled plasmas. A fluid plasma model that includes thermoelectric electron energy transport is used to understand how these structures form. The electron thermoelectric transport coefficient is calculated using Bolsig+ for different chemistries and is found to be large for Ar plasma. Thermoelectric electron energy transport, which is driven by particle diffusion, opposes electron thermal conduction and can localize the plasma, leading to periodic structures. To examine these structures in radio frequency (RF) capacitive plasmas, two-dimensional Ar plasma at 13.5 MHz is first simulated without and then with thermoelectric electron energy transport. The charged species densities are perturbed in the simulations, and the growth or decay of different modes with time is observed. The periodicity of the structure is found to be determined by the relative strength of thermoelectric electron energy transport compared to energy conduction and losses. The effect of operating variables such as chemistry and pressure and design variables such as inter-electrode gap and steps in the electrode have been studied. For Ar plasma as pressure is decreased, the plasma peaks become stronger since thermoelectric electron energy transport is enhanced. Within limits, steps in the electrodes can be used to control the location of the periodic structures. For N2 plasma, the periodic structure does not appear as thermoelectric electron energy transport is weak. The spacing between plasma peaks is found to be dependent on pressure, chemistry, and inter-electrode gap.

The highly complex nanostructured framework of carbon dots (CDs) elevates scientific debates regarding their molecular and electronic structures. Here, we are able to highlight the free electron distribution on surface of newly synthesized Ru(III) and amine (ethylenediamine) doped carbon nano dots, Ru:CNDEDAs by identifying CD+• radical ions produced through photoinduced electron transfer to a model quinone drug, menadione (MQ) using laser flash photolysis corroborated with magnetic field of the order of 0.08 T. Amine passivation renders Ru:CNDEDAs surface to be a potential electron donor, which exhibits distance-dependent rapid electron transfer with MQ by chemical engineering with homocystein thiolactone (HCTL) in physiological condition. This modification is basically executed to mimic the post-translational modification (homocysteinylation) of protein–lysine residues by HCTL. Moreover, the high values of hyperfine splitting constants of CDs calculated from the magnetic field effect indicate the presen...

Carbon dots (CDs) are known to have a wide range of applications, yet our understanding of their structures and chemistry remains uncertain because of their highly complex nanostructured framework. Here we attempt to elucidate the molecular structure and intrinsic mechanisms governing photoluminescence (PL) of CDs by trapping seven visibly distinct colored intermediates that evolved during pyrolytic metamorphosis of citric acid with dopant Ru(III). The “excitation-dependent” PL of doped CDs, Ru:CDs, can be tuned by ethylenediamine (EDA), yielding “excitation-independent” highly fluorescent nanodots, Ru:CNDEDAs. To mimic the optical and chemical properties of CDs, we devise a unique model cocktail comprising multiple fluorogenic molecules that truly supports the existence of chemically switchable conjugated moieties in CDs. We propose a plausible molecular level framework of CDs on the basis of spectroscopic findings and existing literature regarding thermal decomposition of CA. The PL of chemically engine...

Chiral, multipetal gold nanoflowers (AuNFs) with crystalline tips were synthesized in high yield through the reduction of HAuCl4 in water in the presence of preformed core–satellite Ag nanoparticle (AgNP) seeds. High-resolution transmission electron microscopic (HRTEM) images and tomography reveal the actual crystallographic and 3-dimensional structural profile of the AuNFs. In a first demonstration of this kind, a Hg2+/AuNF combination was shown to catalyze the direct transformation of rhodamine-B to rhodamine-110 in water. The AuNFs were also shown to catalyze reduction of nitroarenes to its corresponding aminoarene with ∼90% conversion efficiency by a single-step, one-pot, eco-friendly protocol. There are numerous opportunities for using these unique AuNFs in catalysis, sensing, imaging, drug delivery, and opto-photonics.

Monoamine neurotransmission is key to neuromodulation, but imaging monoamines in live neurons has remained a challenge. Here we show that externally added ortho-phthalaldehyde (OPA) can permeate live cells and form bright fluorogenic adducts with intracellular monoamines (e.g., serotonin, dopamine, and norepinephrine) and with L-DOPA, which can be imaged sensitively using conventional single-photon excitation in a fluorescence microscope. The peak excitation and emission wavelengths (λ_(ex) = 401 nm and λ_(em) = 490 nm for serotonin; λ_(ex) = 446 nm and λ_(em) = 557 nm for dopamine; and λ_(ex) = 446 nm and λ_(em) = 544 nm for norepinephrine, respectively) are accessible to most modern confocal imaging instruments. The identity of monoamine containing structures (possibly neurotransmitter vesicles) in serotonergic RN46A cells is established by quasi-simultaneous imaging of serotonin using three-photon excitation microscopy. Mass spectrometry of cell extracts and of in vitro solutions helps us identify the chemical nature of the adducts and establishes the reaction mechanisms. Our method has low toxicity, high selectivity, and the ability to directly report the location and concentration of monoamines in live cells.

Protein aggregation generally results from association between hydrophobic regions of individual monomers. However, additional mechanisms arising from specific interactions, such as intermolecular disulfide bond formation, may also contribute to the process. The latter is proposed to be the initiating pathway for aggregation of immunoglobulin (IgG), which is essential for triggering its immune response. To test the veracity of this hypothesis, we have employed fluorescence correlation spectroscopy to measure the kinetics of aggregation of IgG in separate experiments either allowing or inhibiting disulfide formation. Fluorescence correlation spectroscopy measurements yielded a diffusion time (τ(D)) of ∼200 µsec for Rhodamine-labeled IgG, corresponding to a hydrodynamic radius (R(H)) of 56 A for the IgG monomer. The aggregation kinetics of the protein was followed by monitoring the time evolution of τ(D) under conditions in which its cysteine residues were either free or blocked. In both cases, the progress curves confirmed that aggregation proceeded via the nucleation-dependent polymerization pathway. However, for aggregation in the presence of free cysteines, the lag times were shorter, and the aggregate sizes bigger, than their respective counterparts for aggregation in the presence of blocked cysteines. This result clearly demonstrates that formation of intermolecular disulfide bonds represents a preferred pathway in the aggregation process of IgG. Fluorescence spectroscopy showed that aggregates formed in experiments where disulfide formation was prevented denatured at lower concentration of guanidine hydrochloride than those obtained in experiments where the disulfides were free to form, indicating that intermolecular disulfide bridging is a valid pathway for IgG aggregation.

We report the photophysical effects of nitric oxide and S-nitrosocysteine on an antibacterial agent, acridine orange, and describe its use in sequential sensing of NO, cysteine and S-nitrosocysteine in a protein, as well as Hg2+. We show that cysteine can play a major role in controlling NO-induced resistance to bacteria.

Adenosine is a naturally occurring purine nucleoside that plays important role in various biochemical processes. We have studied the binding of TNP-Ado (trinitrophenylated-adenosine), a fluorescent analogue of adenosine (which itself is a weak fluorophore), with a model transport protein, bovine serum albumin (BSA). The binding affinity was determined using Fluorescence correlation spectroscopy (FCS) and compared with its value obtained from macroscopic fluorescence spectroscopic studies. Fluorescence and circular dichroism (CD) spectroscopies were employed together with molecular docking study to locate the probable binding site of TNP-Ado on BSA and its effect on the conformation and stability of BSA. Fluorescence studies showed that TNP-Ado binds to BSA in 1:1 stoichiometry via an entropically favoured process. Induced CD spectra revealed that a chiro-optical switching of TNP-Ado occurs upon binding to BSA. Results on urea-induced denaturation of BSA and docking study suggested that the binding site for the ligand is in the hydrophobic subdomain IIA of BSA, consistent with the results of other measurements. This study establishes TNP-Ado as a sensor of hydrophobic regions in proteins like serum albumin, having the capability of detecting a minimum concentration of 140ng/ml protein. FCS measurement of binding interaction of rhodamine-labeled TNP-Ado (RTNP-Ado) with BSA yielded an association constant of KFCS=(1.03±0.06) × 10(4)M(-1). The association constants (Ka) obtained for binding of BSA with rhodamine-free (i.e. TNP-Ado) and rhodamine-labeled (RTNP-Ado) ligands, obtained using the ensemble spectroscopic technique, were (2.3±0.06) × 10(5)M(-1) and (3.4±0.03) × 10(4)M(-1), respectively. The difference between the values of Ka for the free and labeled ligands suggests that fluorescent labeling of small molecules perceptibly interferes with the binding process. On the other hand, the difference in Ka obtained by FCS and ensemble techniques is due to the fact that while the former measures the change in the diffusion constant (i.e. size) of RTNP-Ado upon binding to BSA, the latter focuses on the change of tryptophan emission properties of BSA due to the presence of bound RTNP-Ado.

Amyloid beta (Aβ) aggregation is the likely initiator of Alzheimer's disease (AD), but a molecular level understanding of this process is still lacking. A complicating factor is that aggregation intermediates may be more neurotoxic than the aggregates, but they are difficult to characterize due to their transient nature. Major structural features (dominated by β-sheets) appear to remain conserved from small oligomers to fibrils, providing no specific answers to the puzzle. Single mutations in Aβ linked to early onset AD can potentially provide some clues, but are yet to do so.

Very high frequency (VHF) capacitively coupled plasma (CCP) sources offer several benefits, including low plasma potential, high electron density, and controllable dissociation. However, standing electromagnetic waves can make the spatial structure of VHF plasmas a sensitive function of operating conditions and reactor geometry. This paper discusses how the profile of VHF CCPs can be controlled using an external circuit that modifies the electrical boundary conditions. A 2-D plasma model with external circuit has been used for this study, where networks of passive circuit elements can be connected to different electrodes in the reactor. Plasma simulations have been performed for several combinations of capacitors and inductors. It is found that the external circuit can be used to change the radio-frequency current return path, thereby modifying the plasma profile. In general, the plasma is pulled toward the electrode with an inductive impedance and pushed away from the electrode with a capacitive impedance. These changes in plasma profile are related to the relative voltage and their phase on different electrodes.

Capacitively coupled plasma (CCP) discharges using high frequency (HF) and very high frequency (VHF) sources are widely used for dielectric etching in the semiconductor industry. A two-dimensional fluid plasma model is used to investigate the effects of interelectrode gap on plasma spatial characteristics of both HF and VHF CCPs. The plasma model includes the full set of Maxwell’s equations in their potential formulation. The peak in plasma density is close to the electrode edge at 13.5MHz for a small interelectrode gap. This is due to electric field enhancement at the electrode edge. As the gap is increased, the plasma produced at the electrode edge diffuses to the chamber center and the plasma becomes more uniform. At 180MHz, where electromagnetic standing wave effects are strong, the plasma density peaks at the chamber center at large interelectrode gap. As the interelectrode gap is decreased, the electron density increases near the electrode edge due to inductive heating and electrostatic electron heating, which makes the plasma more uniform in the interelectrode region.

Chemically reactive plasmas operating in the 1 mTorr–10 Torr pressure range are widely used for thin film processing in the semiconductor industry. Plasma modeling has come to play an important role in the design of these plasma processing systems. A number of 3-dimensional (3D) fluid and hybrid plasma modeling examples are used to illustrate the role of computational investigations in design of plasma processing hardware for applications such as ion implantation, deposition, and etching. A model for a rectangular inductively coupled plasma (ICP) source is described, which is employed as an ion source for ion implantation. It is shown that gas pressure strongly influences ion flux uniformity, which is determined by the balance between the location of plasma production and diffusion. The effect of chamber dimensions on plasma uniformity in a rectangular capacitively coupled plasma (CCP) is examined using an electromagnetic plasma model. Due to high pressure and small gap in this system, plasma uniformity is found to be primarily determined by the electric field profile in the sheath/pre-sheath region. A 3D model is utilized to investigate the confinement properties of a mesh in a cylindrical CCP. Results highlight the role of hole topology and size on the formation of localized hot-spots. A 3D electromagnetic plasma model for a cylindrical ICP is used to study inductive versus capacitive power coupling and how placement of ground return wires influences it. Finally, a 3D hybrid plasma model for an electron beam generated magnetized plasma is used to understand the role of reactor geometry on plasma uniformity in the presence of E × B drift.

Protein aggregation generally results from association between hydrophobic regions of individual monomers. However, additional mechanisms arising from specific interactions, such as intermolecular disulfide bond formation, may also contribute to the process. The latter is proposed to be the initiating pathway for aggregation of immunoglobulin (IgG), which is essential for triggering its immune response. To test the veracity of this hypothesis, we have employed fluorescence correlation spectroscopy to measure the kinetics of aggregation of IgG in separate experiments either allowing or inhibiting disulfide formation. Fluorescence correlation spectroscopy measurements yielded a diffusion time (τ(D)) of ∼200 µsec for Rhodamine-labeled IgG, corresponding to a hydrodynamic radius (R(H)) of 56 Å for the IgG monomer. The aggregation kinetics of the protein was followed by monitoring the time evolution of τ(D) under conditions in which its cysteine residues were either free or blocked. In both cases, the progress curves confirmed that aggregation proceeded via the nucleation-dependent polymerization pathway. However, for aggregation in the presence of free cysteines, the lag times were shorter, and the aggregate sizes bigger, than their respective counterparts for aggregation in the presence of blocked cysteines. This result clearly demonstrates that formation of intermolecular disulfide bonds represents a preferred pathway in the aggregation process of IgG. Fluorescence spectroscopy showed that aggregates formed in experiments where disulfide formation was prevented denatured at lower concentration of guanidine hydrochloride than those obtained in experiments where the disulfides were free to form, indicating that intermolecular disulfide bridging is a valid pathway for IgG aggregation.

We introduce a new rhodamine-rhodanine-based "turn-on" fluorescent sensor (RR1) and describe its application for detection of mercury, including in solution, in live cells, and in a living vertebrate organism. The sensor RR1, which is a one-pot synthesis from rhodamine B, undergoes a rapid and irreversible 1:1 stoichiometric reaction with Hg(2+) in aqueous medium. Using fluorescence correlation spectroscopy (FCS), RR1 was shown to detect the presence of as low as a 0.5 pM concentration of Hg(2+). It may also lend itself to tagging with biomolecules and nanoparticles, leading to the possibility of organelle-specific Hg detection. Results of experiments with mammalian cells and zebrafish show that RR1 is cell and organism permeable and that it responds selectively to mercury ions over other metal ions. In addition, real-time monitoring of inorganic mercury ion uptake by cells and live zebrafish using this chemosensor shows that saturation of mercury ion uptake occurs within 20-30 min in cells and organisms. We also demonstrate the acquisition of high-resolution real-time distribution maps of inorganic mercury (Hg(2+)) in the zebrafish brain by using a simple fluorescence confocal imaging technique.

A self-consistent two-dimensional three moment radio-frequency glow discharge model has been developed for methane feed gas using a fluid model to study the charged species dynamics and its effects on deposition in a polyatomic gas discharge. Swarm data as a function of electron energy are provided as input to the model. The discharge is electropositive since positive ion density is more than negative ion density. The importance of two-dimensional modeling has been emphasized by comparing the plasma variables with those of a one-dimensional model. The model predicts both the radial and axial variations of species densities, electron energy and electric field. The off-axis maxima in species densities, typical for two-dimensional discharge, can be observed. The asymmetry of the discharge generates a self dc bias that has been predicted by a trial and error method. The model also calculates the radial variations of species fluxes to the cathode that are important to predict the film deposition.

Summary form only given. Capacitively coupled plasmas in the sub-20 mTorr range have gained importance in recent years for advanced micro-electronic device fabrication. Due to long electron mean free path and large bias voltages in this regime, kinetic effects play an important role in the behavior of low pressure plasmas. To consider the kinetic effects, a 1D hybrid plasma model has been developed that uses particle in cell (PIC) technique [1] for charged species, and the fluid method for neutral species. The PIC model includes Monte Carlo Collision (MCC) method to calculate collision frequencies for various processes using a database of collision cross-sections. The fluid model for neutral species takes into account species transport in the plasma, chemical reactions, and surface processes. Capacitively coupled Ar plasma is simulated at low pressure (5-10 mTorr) at 60 MHz. The rf voltage (200-400 V) has been applied to the right electrode, and the left electrode is grounded. The secondary electron emission coefficient for ions is 0.3 on both electrodes. The inter-electrode gap is varied from 5.0 cm to 2.1 cm. In the plasma, electrons primarily absorb power from the external power supply at the sheath edge during sheath acceleration [2]. Energetic beam electrons are generated at the sheath edge during electron heating, which are responsible for plasma production and sustenance through collisions. With decrease in gap, electron density is first observed to decrease due to increase in surface loss to volume generation ratio. However, as the gap is further narrowed, the electron density starts increasing again. This increase in electron density occurs at a narrow gap as the beam electron transit time from one sheath to the opposite one becomes commensurate with the sheath oscillation period, resulting in enhanced power deposition. The peak in electron density is observed at the narrow gap at different pressures and rf voltages.

Plasma modeling is a critical technology for the design of industrial plasma processing systems. Plasma processes are increasingly being extended to the sub‐20 mTorr regime in the microelectronics industry, requiring accurate plasma models in the low pressure regime. Simultaneously, economic considerations are imposing stringent requirements on plasma uniformity over large substrates and plasma modeling is expected to address these uniformity challenges. These trends are necessitating good theoretical understanding in low temperature plasmas of (a) kinetic phenomena at low pressures and (b) the complex interplay between plasma, electromagnetic, chemical and fluid dynamics phenomena in three dimensions. Several fluid and particle‐in‐cell models are used in this paper to address issues of importance to the design and use of plasma etching and deposition systems.

Multi-frequency capacitively coupled plasma (CCP) sources in the range of 2-180 MHz are widely used for materials processing in the semiconductor industry. Very high frequency (VHF) sources bring various benefits including low plasma potential, high electron density, and controllable dissociation. Sources in the low frequency (LF) and high frequency (HF) regimes provide high ion energy with different ion energy distributions. Multi-frequency CCP reactors have been developed to combine the benefits of both frequency regimes. However, plasma structure can be difficult to control over a wide range of operating conditions (a few mTorr to several hundred mTorr, hundred to several thousand Watts, electropositive and electronegative chemistries). This paper discusses how the plasma structure can be controlled using external circuit impedance that modifies the plasma boundary conditions. A 2-dimensional plasma model with external circuit has been developed and used for this study. The plasma model considers conservation of charge species densities, momentum and energy along with the full set of Maxwell equations. The external circuit is a network of passive circuit elements connected to different electrodes. Plasma simulations have been performed for various external circuit configurations using combinations of capacitors and inductors. We found that the plasma structure and profile can be controlled by changing the current return path impedance. In general, the plasma is pulled towards the electrode with an inductive impedance and pushed away from the electrode with a capacitive impedance. When only capacitors are used, the plasma moves towards the electrode with lower impedance. As a result, the ion flux profile to the electrode can be controlled using the external circuit impedance. Electron density measurements using the resonance cavity method are used to verify that the electron density profile can indeed be modified using the external circuit impedance.

Summary form given only.VHF power is commonly used to generate plasmas for processing applications due to various benefits including low plasma potential and controllable dissociation. However, plasma uniformity can be difficult to control due to its strong dependence on frequency, load conditions (pressure, power, gas mixture electronegativity), reactor geometry and boundary conditions. This paper addresses the use of phase difference and voltage waveform in controlling plasma uniformity. VHF power of the same frequency is applied to 2 different electrodes, and voltage phase is controlled at the electrode. It is demonstrated that phase difference between electrodes (with respect to reference chamber ground) can be used to control plasma uniformity. A 180 degree out of phase condition maximizes the current between the electrodes, providing a relatively center high plasma density. On the other hand, a 0 degree in phase condition minimizes the current between electrodes, providing a center low plasma. In addition to phase, plasma uniformity can be controlled by changing the applied voltage waveform. A sinusoidal waveform at low frequencies predominantly generates edge high plasma. An asymmetric triangular waveform at low frequency generates higher harmonics (e.g., 2nd and 3rd harmonics) that lead to higher density and plasma tills in the chamber center. VHF frequency can be excited at a sub-harmonic of the desired frequency component. For example, if power at f MHz is desired for one of the VHF sources, it may be excited by driving an f/3 MHz generator. The f/3 MHz generator can then be used to excite the plasma with a higher frequency (in this case f MHz) to produce a center-high plasma uniformity profile. Alternatively, ratio of power of the two VHF sources can be selected to minimize the non-uniformity for a recipe or load condition. The two VHF generators can be coupled together to the same or different electrodes to control plasma uniformity.

Summary form only given. In order to minimize chamber contamination, to reduce cleaning time and cost, and to minimize process drift it is crucial to confine plasma in the process chamber preventing plasma penetrating to the downstream chamber. Plasma can be confined using physical confinement ring and/or by impedance confinement. In order to quantify the confinement level, we define the density ratio as the ratio of maximum plasma density below the confinement ring to that in the process chamber. The lower the density ratio, the better the plasma confinement. In order to design plasma confinement ring, plasma simulation has been performed to analyze the effectiveness of various confinement ring designs for a very high frequency capacitively coupled reactor. A confinement ring also increases chamber flow resistance adversely affecting the process window. Flow simulation has been performed to calculate pressure on wafer plane for different confinement ring gap widths. The confinement ring design is optimized not only to confine plasma but also to reduce flow resistance. To further improve the plasma confinement an innovative concept of impedance confinement has been analyzed using plasma simulation. An impedance parameter has been defined, and the density ratio is calculated. The impedance parameter has been optimized so as to achieve highly confined plasma. The impedance parameter can be controlled to increase plasma confinement during etch process, and to decrease plasma confinement during cleaning, as necessary

Summary form only given. Plasma simulation has been performed for a capacitively coupled discharge to study frequency effect on electron density, power deposition, and dissociation fraction. Simulation results demonstrated that plasma production efficiency improves with an increase in frequency while ion bombardment energy diminishes. At very high frequency, plasma generation can be controlled independent of ion energy. A very high frequency source has been developed that generates high-density plasma while RF bias is used to control ion energy. Process data showed that the etch rate for a dual damascene trench etch process increases while damage from ion bombardment is reduced. Simulation of plasma clean demonstrated higher species flux at lower pressure and higher source power. Process data confirmed that plasma cleaning is more efficient under these conditions. Thus, plasma simulation focused the selection of source frequency and helped optimize hardware and process design to make possible an effective all-in-one sequence of main etch, ash, and clean

Low-pressure (

Fluorescence Correlation Spectroscopy (FCS) is a powerful technique for studying the diffusive dynamics of fluorophore-tagged biomolecules and thereby drawing inferences about their conformational states and transitions. We have employed FCS to investigate the denaturation and aggregation pathways of bovine immunoglobulin (IgG), a multi-subunit all beta-sheet Y-shaped protein prone to aggregation. Each upper arm of the Y consists of a light and a heavy chain connected by cysteine-shy;cysteine disulphide bonds, and the two heavy chains are joined at the bend by more disulphides. While majority of proteins show continuous increase of hydrodynamic radius (Rg) when presented with increasing denaturant concentration, IgG exhibits strikingly different behavior under similar conditions. Its Rg initially decreases with increasing concentration of GdnHCl (from 0 to 3 M) and then goes through two pronounced maxima at 4 M and 7 M [GdnHCl]. We propose that the initial contraction is related to sheet-to-helix transition at the flexible bends of the Y-arms of the protein. The first maximum of Rg is attributed to electrostatic repulsions and their screening by Gdn+ and Cl- ions; the second is shown to arise from disulphide-mediated effects.Previous studies have proposed that IgG aggregation is initiated by intermolecular disulphide bond formation. We studied the aggregation kinetics of IgG by monitoring the time evolution of characteristic diffusion time (τD) under two different conditions: with the cysteine residues free to interact or blocked. The progress curves (τD vs.elapsed time) were sigmoidal in both cases, but the delay time was almost an order of magnitude longer, and the apparent polymerization rate half as fast, for the case where the cysteines were blocked than when they were free. This result indicates that intermolecular disulphide bond formation is a key factor driving the aggregation process of IgG.

We report an elegant, facile and green protocol for designing dendrimer-like assemblies of multicolor fluorophore-labeled peptides grafted on AuNPs. The distribution pattern of these fluorescent nanoparticles in neuroblastoma cells is studied to demonstrate their use as endosome markers and further extension to multicolor imaging.

Very high frequency (VHF) capacitively coupled plasma sources are widely used for semiconductor manufacturing processes. Uniform plasma can be difficult to achieve at VHF for different load conditions (pressure, power, gas mixture electronegativity, etc.). This paper discusses how voltage phase difference between top and bottom electrodes can be used to control plasma uniformity above the wafer.

Design of an all-in-one (main etch, PR ash and clean) dielectric etch chamber requires independent control of plasma generation from ion energy. Plasma simulation has been performed for a capacitively coupled discharge to study frequency effect on electron density, power deposition, and dissociation fraction. Simulation results demonstrate that plasma production efficiency enhances with increase in frequency while energy of the bombarding ions diminishes. A very high frequency source has been developed to generate high density plasma while radio frequency bias has been used to control ion energy. As illustrated, the etch rate for a dual damascene trench etch process increases, while damage due to ion bombardment is reduced. The dissociation fraction is well behaved to provide necessary corner protection. High-frequency source was used to achieve better performance for dual damascene trench etch process.

The effect of inhomogeneous magnetic field on the spatial structure of very high frequency (VHF) plasmas is investigated for different coil configurations, gas pressures, high frequency bias powers, and degrees of electronegativity. The simulation results show that the electron density peaks in the center of the chamber for VHF plasmas due to the standing electromagnetic wave effect. On application of a magnetic field, the density increases near the wafer edge and decreases at the chamber center. The radial magnetic field component is found to limit electron loss to the electrodes and locally enhance the electron density. The axial magnetic field component limits plasma diffusion in the radial direction helping preserve the effect of improved electron confinement by the radial magnetic field. The peak electron density decreases with increasing magnetic field as the plasma moves toward the electrode edge occupying a larger volume. The effect of magnetic field becomes weaker at higher pressure due to the in...

A one-dimensional coupled particle-in-cell and fluid model is used to understand power dynamics at low gas pressures in a capacitively coupled Ar discharge. For the range of gas pressure (5?500?mTorr) and excitation frequency (30?120?MHz) examined, the electrons absorb power at the sheath edge during sheath expansion. Energetic electron beams are generated at the edge of the expanding sheath, which are responsible for plasma production and sustenance. These energetic electrons are able to reach the opposite sheath at low gas pressures and return some of their energy during deceleration in the sheath. As a result, peak electron density decreases significantly below 10?mTorr. Above 50?mTorr, peak electron density is relatively insensitive to pressure as beam electrons deposit most of their energy in the plasma bulk. Secondary electron emission is found critical for plasma sustenance at 30?MHz, while sheath electron heating is the dominant electron heating mechanism at higher frequencies.

Very high frequency (VHF) capacitively coupled plasma (CCP) discharges are being employed for dielectric etching due to VHF’s various benefits including low plasma potential, high electron density, and controllable dissociation. If the plasma is generated using multiple VHF sources, one can expect that the interaction between the sources can be important in determining the plasma characteristics. The effects of VHF mixing on plasma characteristics, especially its spatial profile, are investigated using both computational modeling and diagnostic experiments. The two-dimensional plasma model includes the full set of Maxwell equations in their potential formulation. The plasma simulation results show that electron density peaks at the center of the chamber at 180 MHz due to the standing electromagnetic wave. Electrostatic effects at the electrode edges tend to get stronger at lower VHFs such as 60 MHz. When the two rf sources are used simultaneously and power at 60 MHz is gradually increased, the ion flux be...

A two-dimensional plasma model that includes the full set of Maxwell equations is used to understand the physics of very high frequency capacitively coupled plasmas. The effect of radio frequency (RF) source power, inter-electrode gap and gas mixture (Ar, Ar/SF6, Ar/CF4) on the plasma characteristics is investigated. The computational results show that the plasma spatial profile is influenced by both electrostatic and electromagnetic effects. The electrostatic power deposition is stronger at the electrode edges due to electric field enhancement at corners. Therefore, when the electrostatic effects are dominant, the plasma density peaks off-axis. Due to a standing electromagnetic wave in the chamber, the electron density peak moves to the chamber center under conditions where electromagnetic effects become strong. Inductive heating due to the radial electromagnetic electric field can also influence the plasma spatial profile. The relative importance of electromagnetic and electrostatic effects is found to be a function of the RF source power, the inter-electrode gap and the plasma electronegativity. While the electron density peaks on-axis at a low source power, inductive power deposition at higher source powers shifts the electron density peak towards the electrode edge. Electrostatic power deposition makes the plasma more uniform at smaller inter-electrode gaps. Due to a lower electron density and a larger applied RF potential, electrostatic effects become more dominant in electronegative discharges.